Structure of PDB 2opf Chain A Binding Site BS02

Receptor Information

>2opf Chain A (length=256) Species: 562 (Escherichia coli)

PEGPEIRRAADNLEAAIKGKPLTDVWFAFPQLKTYQSQLIGQHVTHVETR
GKALLTHFSNDLTLYSHNQLYGVWRVVDTGEEPQTTRVLRVKLQTADKTI
LLYSASDIEMLRPEQLTTHPFLQRVGPDVLDPNLTPEVVKERLLSPRFRN
RQFAGLLLDQAFLAGLGNYLRVEILWQVGLTGNHKAKDLNAAQLDALAHA
LLEIPRFSYATRGQVDALFRFKVFHRDGEPCERCGSIIEKTTLSSAPFYW
CPGCQH

Ligand information

>2opf Chain C (length=12)

caggacgaagcc

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2opf Active site plasticity of endonuclease VIII: Conformational changes compensating for different substrates and mutations of critical residues
• Resolution: 1.85 Å
• Binding residue (original residue number in PDB): P1 E2 K52 H67 Q69 L70 F121 Q160 G167 F230 H231 P253
• Binding residue (residue number reindexed from 1): P1 E2 K52 H67 Q69 L70 F121 Q160 G167 F224 H225 P247

Enzymatic activity

• Enzyme Commision number: 3.2.2.-
  4.2.99.18: DNA-(apurinic or apyrimidinic site) lyase.

Gene Ontology

Molecular Function

• GO:0000703 oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity
• GO:0003676 nucleic acid binding
• GO:0003677 DNA binding
• GO:0003684 damaged DNA binding
• GO:0003906 DNA-(apurinic or apyrimidinic site) endonuclease activity
• GO:0008270 zinc ion binding
• GO:0016787 hydrolase activity
• GO:0016798 hydrolase activity, acting on glycosyl bonds
• GO:0016799 hydrolase activity, hydrolyzing N-glycosyl compounds
• GO:0016829 lyase activity
• GO:0019104 DNA N-glycosylase activity
• GO:0046872 metal ion binding
• GO:0140078 class I DNA-(apurinic or apyrimidinic site) endonuclease activity

Biological Process

• GO:0006281 DNA repair
• GO:0006284 base-excision repair

External links

• PDB: RCSB:2opf, PDBe:2opf, PDBj:2opf
• PDBsum: 2opf
• UniProt: P50465|END8_ECOLI Endonuclease 8 (Gene Name=nei)